Hello,

I was running Annovar to annotate snps and indels. While checking the assigned information of potentially pathogenic mutations I discovered that rs number from avdbsnp144 is not compatible with chromosome coordinates. Example below.

48878115        48878117    CCG    -    exonic    RB1    rs587778823

According to dbSNP rs587778823 represents 48878120-48878122 coordinates, and it's assigned as "with pathogenic allele". But this is not my deletion!

So, I was checking what could be wrong. I found that deletion with presented coordinates (48878115-48878117) has rs760927237 (not pathogenic!). But it is not what Annovar annotated.

First, I thought that maybe it's the reverse and forward strand differences -- no, RB1 is on forward strand.

Second, I looked at hg19_avsnp144.txt downloaded from annovar web page. And here is what I found:

13    48878115    48878115    CCG    -    rs587778823
13    48878115    48878115    CCG    -    rs760927237

Can anybody explain why deletion has two rs number with different clinical significance?

Is it possible to make annovar write in output both rs numbers?

I would appreciate for any help,

Agata